The bushings seemed to be in "good enough" condition. I suspect that they're probably just to reduce turbulence and the amount of crossover between the runners.

I can't really believe that they're for mechanical support, since that would have meant that Mikuni engineered a rubber-to-aluminum bushing interface.

I could be wrong...are there actually any documented instances of these shafts breaking due to vibration fatigue?

It seems to me that with the butterflies open, they would have a pretty small cross section to the airflow, reducing the possibility of intake pulse induced vibration...and when they are closed, the butterflies are basically braced against the walls of the intake. On top of that, just bolting the butterflies to the shaft would help stiffen up the whole assembly.

And yes, I am of the thinking that things are engineered the way they are for a reason. I'm sure there's either a performance or economy benefit, if not both, to having the butterfly setup functioning. I mean, that's a fairly complex setup that undoubtedly added significant initial cost to the engine, plus the additional parts count and potential points of failure...I don't think an auto manufacturer would put that on there without good reason.